RnBeads (version 1.4.0)

performEnrichment.diffMeth: performEnrichment.diffMeth

Description

performs Geno Ontology (GO) enrichment analysis for a given differential methylation table.

Usage

performEnrichment.diffMeth(rnbSet, diffmeth, ontologies = c("BP", "MF"), rank.cuts.region = c(100, 500, 1000), add.auto.rank.cut = TRUE, rerank = TRUE, verbose = TRUE, ...)

Arguments

rnbSet

RnBSet object for which dirrential methylation was computed

diffmeth

RnBDiffMeth object. See RnBDiffMeth-class for details.

ontologies

GO ontologies to use for enrichment analysis

rank.cuts.region

Cutoffs for combined ranking that are used to determine differentially methylated regions

add.auto.rank.cut

flag indicating whether an automatically computed cut-off should also be considered.

rerank

For deterimining differential methylation: should the ranks be ranked again or should the absolute ranks be used.

verbose

Enable for detailed status report

...

arguments passed on to the parameters of GOHyperGParams from the GOstats package

Value

a DiffMeth.enrich object (S3) containing the following attributes

region

Enrichment information for differential methylation on the region level. See GOHyperGresult from the GOstats package for furthert details

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment"))
res <- performEnrichment.diffMeth(rnb.set.example,dm)